I am >2% owner of s-corp. My wife also is an employee. In december 2009, Company has made an advance payment of $1000 to the Health Insurance Compay for our health insurance premiums for January 2010. All other premium payments for 2009 went into my W2 Line 14 as S-Corp Meical Insurance. How can I take care of this extra $1000 in my taxes (Both 1120S and my personal 1040)?
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You are talking about two different things here If the company paid an advance of $1,000 that has nothing to do with you or your W2 - you didn't actually pay it yourself. The amount you pay shows up on your W2 and when it comes out of your pay it is credited to an arbitrary account that the billing has been entered under - if the company made an advance payment it would be charged to "Prepaid Insurance" in your COMPANY balance sheet. This would not show up in your payroll check as a deduction at all.
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